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BioC 3.5: CHECK report for BubbleTree on tokay2

This page was generated on 2017-10-18 14:24:26 -0400 (Wed, 18 Oct 2017).

Package 156/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BubbleTree 2.6.0
Todd Creasy , Wei Zhu , Kui Shen
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/BubbleTree
Branch: RELEASE_3_5
Last Commit: 2f97875
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BubbleTree
Version: 2.6.0
Command: rm -rf BubbleTree.buildbin-libdir BubbleTree.Rcheck && mkdir BubbleTree.buildbin-libdir BubbleTree.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BubbleTree.buildbin-libdir BubbleTree_2.6.0.tar.gz >BubbleTree.Rcheck\00install.out 2>&1 && cp BubbleTree.Rcheck\00install.out BubbleTree-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BubbleTree.buildbin-libdir --install="check:BubbleTree-install.out" --force-multiarch --no-vignettes --timings BubbleTree_2.6.0.tar.gz
StartedAt: 2017-10-17 22:27:10 -0400 (Tue, 17 Oct 2017)
EndedAt: 2017-10-17 22:35:52 -0400 (Tue, 17 Oct 2017)
EllapsedTime: 522.5 seconds
RetCode: 0
Status:  OK  
CheckDir: BubbleTree.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf BubbleTree.buildbin-libdir BubbleTree.Rcheck && mkdir BubbleTree.buildbin-libdir BubbleTree.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BubbleTree.buildbin-libdir BubbleTree_2.6.0.tar.gz >BubbleTree.Rcheck\00install.out 2>&1 && cp BubbleTree.Rcheck\00install.out BubbleTree-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=BubbleTree.buildbin-libdir --install="check:BubbleTree-install.out" --force-multiarch --no-vignettes --timings BubbleTree_2.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/BubbleTree.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BubbleTree/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'BubbleTree' version '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'BubbleTree' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 24.7Mb
  sub-directories of 1Mb or more:
    data  22.9Mb
    doc    1.6Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ...It is recommended to use 'given' instead of 'middle'.
 OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
** checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annoByOverlap,Annotate: no visible binding for global variable
  'queryHits'
Undefined global functions or variables:
  queryHits
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeRBD         19.36   0.03   20.48
heteroLociTrack  7.22   0.22    7.44
saveXLS          0.19   0.02   15.67
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
makeRBD         23.78   0.02   23.80
heteroLociTrack  9.40   0.32    9.73
info             5.14   0.03    5.17
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/BubbleTree.Rcheck/00check.log'
for details.


BubbleTree.Rcheck/00install.out:


install for i386

* installing *source* package 'BubbleTree' ...
It is recommended to use 'given' instead of 'middle'.
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'BubbleTree' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BubbleTree' as BubbleTree_2.6.0.zip
* DONE (BubbleTree)

BubbleTree.Rcheck/examples_i386/BubbleTree-Ex.timings:

nameusersystemelapsed
Annotate000
BTreePlotter0.280.060.34
BTreePredictor0.020.000.01
RBD000
RscoreTrack0.700.070.77
TrackPlotter000
annoByGenesAndCyto1.070.031.10
bafTrack1.090.031.12
btcompare000
btpredict3.130.143.27
drawBTree0.530.060.59
drawBubbles0.510.030.55
drawFeatures1.970.001.97
getTracks0.830.000.82
heteroLociTrack7.220.227.44
info3.860.033.89
loadRBD0.090.000.10
makeRBD19.36 0.0320.48
saveXLS 0.19 0.0215.67
trackBTree0.440.000.44
xyTrack0.340.000.34

BubbleTree.Rcheck/examples_x64/BubbleTree-Ex.timings:

nameusersystemelapsed
Annotate000
BTreePlotter0.370.000.39
BTreePredictor0.020.000.02
RBD000
RscoreTrack0.910.020.92
TrackPlotter000
annoByGenesAndCyto1.480.011.50
bafTrack0.750.030.79
btcompare0.020.000.01
btpredict4.200.024.30
drawBTree0.440.010.45
drawBubbles0.380.020.39
drawFeatures2.030.022.05
getTracks1.330.001.33
heteroLociTrack9.400.329.73
info5.140.035.17
loadRBD0.110.020.13
makeRBD23.78 0.0223.80
saveXLS0.170.000.76
trackBTree0.540.010.55
xyTrack0.360.000.36